Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics.

ABSTRACT: The behaviour of biomolecular systems is governed by their thermodynamic and kinetic properties. It is thus important to be able to calculate, for example, both the affinity and rate of binding and dissociation of a protein-ligand complex, or the populations and exchange rates between distinct conformational states. Because these are typically rare events, calculating these properties from long molecular dynamics simulations remains extremely difficult. Instead, one often adopts a divide-and-conquer strategy in which equilibrium free-energy differences and the fastest state-to-state transition (e.g. ligand association or minor-to-major state conversion) are combined to estimate the slow rate (e.g. ligand dissociation) using a two-state assumption. Here we instead address thes

SUBMITTER: Wang Y 

PROVIDER: S-EPMC5859887 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature